When the following inclusion / exclusion types are specified in the analysis properties at project level, they must be relative to the project / analysis root: source files, test files, coverage, and duplications. Paths specified at project level will continue to be re-applied at module level but will raise a warning. This backward-compatibile behavior is considered deprecated and will be dropped in a future version.

The first bullet point misses sonar.issue.ignore.multicriteria and sonar.issue.enforce.multicriteria. Both will raise a warning if the path is not relative to the project root.

The second bullet point is OK, but sonar.sourceEncoding does not raise a warning if defined on module level. It is simply ignored, while for the rest, you will see a warning. You might have wanted to warn for this property too? Either way, the current behavior is somewhat confusing, and not documented.